[SOLVED] Build problem for AdvancedFEM plugin

[amazier]

Hi all,

I am currently trying to update an old plugin to use advanced FEM models. After spending some time generating the Cmake list (thanks to Hugo!), I encountered some errors on the build. I am compiling with GCC 9.

/home/arnaud/dev/sofa/v20.06/src/applications/plugins/SofaAdvancedFEM/SofaAdvancedFEM/NonFoldingTetrahedralConstraint.cpp:58: error: explicit instantiation of 'NonFoldingTetrahedralConstraint' does not refer to a function template, variable template, member function, member class, or static data member

The code is the following where the object is normally added to the factory and I do not understand what is done wrongly.

SOFA_DECL_CLASS(NonFoldingTetrahedralConstraint)

int NonFoldingTetrahedralConstraintClass = core::RegisterObject("Remove Folding Tetrahedra")
#ifndef SOFA_FLOAT
        .add< NonFoldingTetrahedralConstraint<Vec3dTypes> >()
#endif
#ifndef SOFA_DOUBLE
        .add< NonFoldingTetrahedralConstraint<Vec3fTypes> >()
#endif
        ;

#ifndef SOFA_FLOAT
template class SOFA_ADVANCED_FEM_API NonFoldingTetrahedralConstraint<Vec3dTypes>;
#endif
#ifndef SOFA_DOUBLE
template class SOFA_ADVANCED_FEM_API NonFoldingTetrahedralConstraint<Vec3fTypes>;
#endif

If I comment the template function, I obtain an error on the library that I do not understand…

FAILED: lib/libSofaAdvancedFEM.so.0.1 
: && /usr/bin/g++ -fPIC -Wall -W -Wno-padded   -shared -Wl,-soname,libSofaAdvancedFEM.so.0.1 -o lib/libSofaAdvancedFEM.so.0.1 applications/plugins/SofaAdvancedFEM/SofaAdvancedFEM/CMakeFiles/SofaAdvancedFEM.dir/initAdvancedFEM.cpp.o applications/plugins/SofaAdvancedFEM/SofaAdvancedFEM/CMakeFiles/SofaAdvancedFEM.dir/NonFoldingTetrahedralConstraint.cpp.o applications/plugins/SofaAdvancedFEM/SofaAdvancedFEM/CMakeFiles/SofaAdvancedFEM.dir/AdhesiveSurfaceForceField.cpp.o applications/plugins/SofaAdvancedFEM/SofaAdvancedFEM/CMakeFiles/SofaAdvancedFEM.dir/TetrahedralBiquadraticSpringsForceField.cpp.o applications/plugins/SofaAdvancedFEM/SofaAdvancedFEM/CMakeFiles/SofaAdvancedFEM.dir/TetrahedralQuadraticSpringsForceField.cpp.o applications/plugins/SofaAdvancedFEM/SofaAdvancedFEM/CMakeFiles/SofaAdvancedFEM.dir/FastHexahedralCorotationalForceField.cpp.o applications/plugins/SofaAdvancedFEM/SofaAdvancedFEM/CMakeFiles/SofaAdvancedFEM.dir/TetrahedralTotalLagrangianForceField.cpp.o applications/plugins/SofaAdvancedFEM/SofaAdvancedFEM/CMakeFiles/SofaAdvancedFEM.dir/TetrahedralStVenantKirchhoffForceField.cpp.o applications/plugins/SofaAdvancedFEM/SofaAdvancedFEM/CMakeFiles/SofaAdvancedFEM.dir/NeoHookeanForceField.cpp.o applications/plugins/SofaAdvancedFEM/SofaAdvancedFEM/CMakeFiles/SofaAdvancedFEM.dir/MRForceField.cpp.o applications/plugins/SofaAdvancedFEM/SofaAdvancedFEM/CMakeFiles/SofaAdvancedFEM.dir/TriangleMomentForceField.cpp.o  -Wl,-rpath,/home/arnaud/dev/sofa/v20.06/build3/lib:  -lSofaComponentBase  lib/libSofaUserInteraction.so.20.06.99  lib/libSofaMiscForceField.so.20.06.99  lib/libSofaMiscFem.so.20.06.99  lib/libSofaGeneralMeshCollision.so.20.06.99  lib/libSofaMeshCollision.so.20.06.99  lib/libSofaObjectInteraction.so.20.06.99  lib/libSofaRigid.so.20.06.99  lib/libSofaBaseCollision.so.20.06.99  lib/libSofaGeneralRigid.so.20.06.99  lib/libSofaBaseMechanics.so.20.06.99  lib/libSofaGeneralVisual.so.20.06.99  lib/libSofaTopologyMapping.so.20.06.99  lib/libSofaGraphComponent.so.20.06.99  lib/libSofaSimulationTree.so.20.06.99  lib/libSofaBaseUtils.so.20.06.99  lib/libSofaBaseVisual.so.20.06.99  lib/libSofaDeformable.so.20.06.99  lib/libSofaBoundaryCondition.so.20.06.99  lib/libSofaEigen2Solver.so.20.06.99  lib/libSofaBaseLinearSolver.so.20.06.99  lib/libSofaMiscTopology.so.20.06.99  /usr/lib/x86_64-linux-gnu/libz.so  lib/libSofaGeneralTopology.so.20.06.99  lib/libSofaSimpleFem.so.20.06.99  lib/libSofaBaseTopology.so.20.06.99  lib/libSofaSimulationCommon.so.20.06.99  lib/libSofaSimulationCore.so.20.06.99  lib/libSofaCore.so.20.06.99  lib/libSofaDefaultType.so.20.06.99  lib/libSofaHelper.so.20.06.99  /usr/lib/x86_64-linux-gnu/libGLU.so  /usr/lib/x86_64-linux-gnu/libGLX.so  /usr/lib/x86_64-linux-gnu/libOpenGL.so  /usr/lib/x86_64-linux-gnu/libGLEW.so  /usr/lib/x86_64-linux-gnu/libboost_system.so  /usr/lib/x86_64-linux-gnu/libboost_filesystem.so  /usr/lib/x86_64-linux-gnu/libboost_program_options.so  /usr/lib/x86_64-linux-gnu/libboost_thread.so  /usr/lib/x86_64-linux-gnu/libboost_chrono.so  /usr/lib/x86_64-linux-gnu/libboost_date_time.so  /usr/lib/x86_64-linux-gnu/libboost_atomic.so  lib/libgtest.so.2.6.2  -pthread  lib/libnewmat.a  -Wl,-rpath-link,/home/arnaud/dev/sofa/v20.06/build3/lib && :
/usr/bin/ld: cannot find -lSofaComponentBase
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.

Thanks for your help and have a nice day,

[Froy]

For your first error, please give some more information from your class NonFoldingTetrahedralConstraint
But 🧐:
– there is no more compilation (by default) of Vec3fTypes (no more #ifndef SOFA_DOUBLE …)
– SofaComponentBase has been renamed one or two releases ago (?), now this package is called SofaBase. So you will need to link against SofaBase (instead of SofaComponentBase)

[amazier]

Hi Froy,
Thank you for your super quick answer!
The first error is not urgent for the moment but I will ping you if I cannot solve the issue.
As for the second one, indeed, replacing SofaComponentBase by SofaBase in the Cmake fixed the issue of the build 😉

Once the build is done, I am running runSofa and obtain the following error:

[ERROR]   [PluginManager] Plugin loading failed (/home/arnaud/dev/sofa/v20.06/build3/lib/libSofaAdvancedFEM.so): /home/arnaud/dev/sofa/v20.06/build3/lib/libSofaAdvancedFEM.so: undefined symbol: _ZNK4sofa9component8topology30NumericalIntegrationDescriptorIfLi3EE19getQuadratureMethodENS3_16QuadratureMethodEm
[ERROR]   [PluginManager] Plugin not found: "Modeler"
Warning: Setting a new default format with a different version or profile after the global shared context is created may cause issues with context sharing.
The constructor with a QGLFormat is deprecated, use the regular contructor instead.

So for Modeler, I suppose maybe it is not supported anymore or has been replaced. As for the second one, I have no idea why the lib has such undefined symbol.. Do you have any idea?

EDIT: I cleaned the Cmake file and got rid of the Modeler
Merci

[Froy]

According to the demangler,
You would need the definition of

sofa::component::topology::NumericalIntegrationDescriptor<float, 3>::getQuadratureMethod(sofa::component::topology::NumericalIntegrationDescriptor<float, 3>::QuadratureMethod, unsigned long) const

And this NumericalIntegrationDescriptor is currently only compiled with double (BaseTopology/NumericalIntegrationDescriptor.cpp)

Therefore, you will need to add the templated definition with

#include <SofaBaseTopology/NumericalIntegrationDescriptor.inl>

to be able to instanciate with new templated class with float

[amazier]

Thank you for your answer Froy!
Now it is done but I am bumping into another obstacle when I am running SOFA:

terminate called after throwing an instance of 'std::logic_error'
  what():  basic_string::_M_construct null not valid

########## SIG 6 - SIGABRT: usually caused by an abort() or assert() ##########
-> /home/arnaud/dev/sofa/v20.06/build2/lib/libSofaHelper.so.20.06.99(sofa::helper::BackTrace::dump()+0x27) [0x7f417169c2b7]
-> /home/arnaud/dev/sofa/v20.06/build2/lib/libSofaHelper.so.20.06.99(sofa::helper::BackTrace::sig(int)+0x1d6) [0x7f417169c656]
-> /lib/x86_64-linux-gnu/libc.so.6(+0x46210) [0x7f4171168210]
-> /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xcb) [0x7f417116818b]
-> /lib/x86_64-linux-gnu/libc.so.6(abort+0x12b) [0x7f4171147859]
-> /lib/x86_64-linux-gnu/libstdc++.so.6(+0x9e951) [0x7f41713cd951]
-> /lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa47c) [0x7f41713d947c]
-> /lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa4e7) [0x7f41713d94e7]
-> /lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa799) [0x7f41713d9799]
-> /lib/x86_64-linux-gnu/libstdc++.so.6(std::__throw_logic_error(char const*)+0x41) [0x7f41713d025e]
-> /home/arnaud/dev/sofa/v20.06/build2/lib/libSofaHelper.so.20.06.99(sofa::helper::system::PluginManager::checkDuplicatedPlugin(sofa::helper::system::Plugin const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xad4) [0x7f4171757894]
-> /home/arnaud/dev/sofa/v20.06/build2/lib/libSofaHelper.so.20.06.99(sofa::helper::system::PluginManager::loadPluginByPath(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::ostream*)+0x10eb) [0x7f417175ab2b]
-> /home/arnaud/dev/sofa/v20.06/build2/lib/libSofaHelper.so.20.06.99(sofa::helper::system::PluginManager::loadPluginByName(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool, std::ostream*)+0x70) [0x7f417175c170]
-> /home/arnaud/dev/sofa/v20.06/build2/lib/libSofaHelper.so.20.06.99(sofa::helper::system::PluginManager::readFromIniFile(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x646) [0x7f417175d826]
-> ./runSofa(+0x157a6) [0x55cf77f917a6]
-> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f41711490b3]
-> ./runSofa(+0x168ce) [0x55cf77f928ce]
Aborted (core dumped

A problem with the plugin name?

[Froy]

First time I see this error 😅
According to the code, PluginManager calls the function
getModuleName()
from your plugin (without checking if it is defined by the dll 😑).

So I suppose there is a problem with this function in your plugin (not defined ? nullptr?)

[amazier]

Hi Froy,

Indeed, I did not include the getModuleName() in the init.cpp!
Now I can properly load the plugin and use it, many thanks!

I still have a little interrogation.
When I am running SOFA I obtain the following message:

[INFO]    [PluginManager] Loaded plugin: /home/arnaud/dev/sofa/v20.06/build3/lib/libSofaAdvancedFEM.so
[INFO]    [PluginManager] Plugin not found in loaded plugins: SofaAdvancedFEM 

Which states that SOFA loaded the plugin but did not find it. But I can actually use without any problem the object of my plugin… Do you have any idea why?

Thank you again,

[Hugo]

Strange. Indeed it seems well loaded.. the second [INFO] is weird.
Any idea @froy? is that related to the recent work on isLoaded?

Hugo

[Froy]

No idea; can you tell us the version of SOFA ? (master, release, etc)

[amazier]

Hi Froy and Hugo,

Sorry I was not connected this weekend.
For my SOFA version, I am on the master branch but did not pull for a while.
I am trying a pull and will let you know.

Best,

[amazier]

Little update:
By pulling, many DEPRECATED arise and I have some issue for compiling just SOFA (on STL mesh if I remember) so I think it is maybe not suitable to be up to date.
Here is the last commit that I have on master:

commit 97060f71c42287699823c7d3548d06c8c4ef8af7 (HEAD -> master)
Merge: 2bf81d557a 1be78658a5
Author: Guillaume Paran <guillaume.paran@sofa-framework.org>
Date:   Mon Nov 2 14:43:12 2020 +0100

    Merge pull request #1563 from fredroy/modularize_general_animloop
    
    [SofaGeneral] Pluginize SofaGeneralAnimationLoop

Best,

[Froy]

2-3 weeks ago, a PR related to this issue has been merged.
https://github.com/sofa-framework/sofa/pull/1615
It may solve this error. 🤔

[Hugo]

Hey @amazier

Has Fred’ s suggestion helped?

[amazier]

Hi Hugo,
Sorry for not having given any news…
Unfortunately, I tried to merge the PM on my SOFA but it did not work.

Best,
Arnaud

[Hugo]

Hey @amazier

Sorry for not being responsive. We will be more available now.
Did you update your SOFA master branch since then?
Do you still have this strange message in PluginManager? I guess it prevents your from using any class from the plugin, is it?

Best wishes,

Hugo

[amazier]

Hi Hugo,

I tried to update my branch 1 month ago but it did not work. Do you want me to try on the new release branch?
I still have this strange message but the thing is that I can still use my plugin’s class. So, in the end, it is not a big problem, it was just to let you know that I had this message despite my working plugin 🙂

No problem, have a nice weekend,
Arnaud

[Hugo]

If it is not a blocking point, it is fine for me: this plugin being a private plugin I can not access it and help you debugging it.

I would bet for a CMakeLists.txt issue. If you want to investigate the fix, you can get inspired for other CMakeLists.txt as in Cosserat plugin for instance. If not, I let you close the topic.

Best wishes.

Hugo

[amazier]

Hi Hugo,

Yes, no problem for me the plugin is working fine. I just found the message a bit strange given that it was working fine 🙂
I am closing the topic, thanks again for your help SOFA consortium!

Best,
Arnaud

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